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Related Concept Videos

Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Overview
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RNA Structure01:23

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Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...

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Nucleocapsid Annealing-Mediated Electrophoresis (NAME) Assay Allows the Rapid Identification of HIV-1 Nucleocapsid Inhibitors
08:33

Nucleocapsid Annealing-Mediated Electrophoresis (NAME) Assay Allows the Rapid Identification of HIV-1 Nucleocapsid Inhibitors

Published on: January 19, 2015

Single-stranded RNA facilitates nucleocapsid: APOBEC3G complex formation.

Hal P Bogerd1, Bryan R Cullen

  • 1Center for Virology, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Duke University, Durham, North Carolina 27710, USA.

RNA (New York, N.Y.)
|May 6, 2008
PubMed
Summary
This summary is machine-generated.

Single-stranded RNA containing guanine residues is essential for APOBEC3G binding to HIV Gag NC protein. This RNA binding is crucial for packaging APOBEC3G into HIV virions, influencing its antiviral activity.

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Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

Area of Science:

  • Virology
  • Molecular Biology
  • Biochemistry

Background:

  • APOBEC3G is an antiretroviral factor selectively packaged into human immunodeficiency virus (HIV) virions.
  • This packaging is thought to be initiated by the binding of APOBEC3G to the nucleocapsid (NC) domain of the HIV Gag polyprotein.
  • Previous studies indicated that RNA mediates this critical interaction.

Purpose of the Study:

  • To investigate the role of RNA binding in the initiation of APOBEC3G:NC complex formation.
  • To determine the specific nucleic acid requirements for APOBEC3G binding to the HIV NC domain.
  • To explore the potential for APOBEC3G to adopt different conformational states based on nucleic acid interactions.

Main Methods:

  • In vitro reconstitution assays using purified, RNase-treated APOBEC3G and NC proteins.
  • Add-back experiments with various types of nucleic acids (ssRNAs, dsRNAs, ssDNAs, dsDNAs, DNA:RNA hybrids, structured RNAs).
  • Assessment of APOBEC3G:NC complex formation in response to different nucleic acid conditions.

Main Results:

  • Complex formation between APOBEC3G and NC protein requires RNA binding by APOBEC3G.
  • Short single-stranded RNAs (ssRNAs) with guanine residues (G) effectively rescued complex formation.
  • Neither ssRNAs lacking G, dsRNAs, ssDNAs, dsDNAs, nor DNA:RNA hybrids induced complex formation.
  • While some structured RNAs (tRNAs, rRNAs) did not rescue binding, others (human Y RNAs, 7SL RNA) did, indicating ssRNA can be part of a structured molecule.
  • These findings suggest APOBEC3G may exist in distinct conformational states when bound to ssRNA versus ssDNA.

Conclusions:

  • Single-stranded RNA, particularly with guanine residues, is essential for initiating the binding of APOBEC3G to the HIV NC domain.
  • The interaction can occur even when the ssRNA is part of a larger, structured RNA molecule.
  • The differential binding to ssRNA and ssDNA suggests APOBEC3G may possess distinct functional states, impacting its activity within the virion.